Research workbench
Psychrobacter arcticus atpprt (hisgz) R56A mutant bound to ATP and prpp
Analyse Psychrobacter arcticus atpprt (hisgz) R56A mutant bound to ATP and prpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Z6R
- Type
- protein
- Length
- 1,157 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP phosphoribosyltransferase regulatory subunit; ATP phosphoribosyltransferase
- EC
- 2.4.2.17
- UniProt
- Q4FTX3, Q4FQF7
- Ligands
- ATP, PRP
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP phosphoribosyltransferase regulatory subunit | protein | 368 | 39% helix, 23% strand | Q4FTX3 |
| B | ATP phosphoribosyltransferase regulatory subunit | protein | 377 | 42% helix, 23% strand | Q4FTX3 |
| C | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 206 | 33% helix, 33% strand | Q4FQF7 |
| D | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 206 | 33% helix, 31% strand | Q4FQF7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, D
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.80 | 0.98 | 25 | empty |
| 2 | 239 | 0.79 | 0.92 | 56 | empty |
| 3 | 524 | 0.76 | 0.84 | 72 | empty |
| 4 | 803 | 0.75 | 0.80 | 64 | empty |
| 5 | 77 | 0.70 | 0.94 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3050 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1033 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 545 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 33 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7Z6R · Psychrobacter arcticus ATPPRT (HisGZ) R56A mutant bound to ATP and PRPP · the same entry in another collection · chain D against D, TM-score 1.00
- Q4FQF7 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase (Q4FQF7) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q4FTX3 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase regulatory subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q4FTX3
- Every structure of UniProt Q4FQF7
- Elsewhere: RCSB PDB 7Z6R · PDBe 7Z6R · UniProt Q4FTX3 · UniProt Q4FQF7
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